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. 2005 Jun;79(11):7024–7041. doi: 10.1128/JVI.79.11.7024-7041.2005

FIG. 5.

FIG. 5.

5′-terminal deletions of domain I maintain remaining cloverleaf structure as assessed by chemical modification. (A-C) Chemically modified sites for nt 1 to 104 of CVB3/28 (A), nt 1 to 93 of TD8 (B), and nt 1 to 51 of TD50 (C). Arrows indicate sites of kethoxal (gray arrows with dots at ends), DMS (black arrows), and CMCT (open arrows) modification. (D) Representative 12% sequencing gel of primer extension for domain 1 on RNA samples using primer PE108. RNA was prepared in vitro from subclones containing the 5′ NTRs of pRibozCVB3/28 (CVB3/28), pRibozCVB3/TD8 (CVB3/TD8), and pRibozCVB3/TD50 (CVB3/TD50). Un, unmodified RNA; K, kethoxal-modified RNA; D, DMS-modified RNA; C, CMCT-modified RNA. Representative modified positions are indicated. Primer extension with dideoxynucleotides was also performed to generate a sequence ladder (U, G, C, A).